EG307 polynucleotides and uses thereof

a technology of eg307 and polynucleotides, applied in the field of eg307 polynucleotides, can solve the problems of difficult identification of such polynucleotides among the tens of thousands of genes in the plant and animal genom

Inactive Publication Date: 2007-08-07
EVOLUTIONARY GENOMICS LLC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0029]In another aspect, the subject invention provides a method for correlating an evolutionarily neutral nucleotide change to a commercially or aesthetically relevant trait that is unique, enhanced or altered in a domesticated organism, comprising: a) ide

Problems solved by technology

While it is desired to identify polynucleotides that control valuable traits, it is challenging t

Method used

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  • EG307 polynucleotides and uses thereof
  • EG307 polynucleotides and uses thereof
  • EG307 polynucleotides and uses thereof

Examples

Experimental program
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Effect test

example 1

cDNA Library Construction

[0284]A domesticated plant or animal cDNA library is constructed using an appropriate tissue from the plant or animal. A person of ordinary skill in the art would know the appropriate tissue or tissues to analyze according to the trait of interest. Alternately, the whole organism may be used. For example, 1 day old plant seedlings are known to express most of the plant's genes.

[0285]Total RNA is extracted from the tissue (RNeasy kit, Quiagen; RNAse-free Rapid Total RNA kit, 5 Prime-3 Prime, Inc., or any similar and suitable product) and the integrity and purity of the RNA are determined according to conventional molecular cloning methods. Poly A+ RNA is isolated (Mini-Oligo(dT) Cellulose Spin Columns, 5 Prime-3 Prime, Inc., or any similar and suitable product) and used as template for the reverse-transcription of cDNA with oligo (dT) as a primer. The synthesized cDNA is treated and modified for cloning using commercially available kits. Recombinants are then...

example 2

Sequence Comparison

[0286]Randomly selected ancestor cDNA clones from the cDNA library are sequenced using an automated sequencer, such as an ABI 377 or MegaBACE 1000 or any similar and suitable product. Commonly used primers on the cloning vector such as the M13 Universal and Reverse primers are used to carry out the sequencing. For inserts that are not completely sequenced by end sequencing, dye-labeled terminators or custom primers can be used to fill in remaining gaps.

[0287]The detected sequence differences are initially checked for accuracy, for example by finding the points where there are differences between the domesticated and ancestor sequences; checking the sequence fluorogram (chromatogram) to determine if the bases that appear unique to the domesticated organism correspond to strong, clear signals specific for the called base; checking the domesticated organism's hits to see if there is more than one sequence that corresponds to a sequence change; and other methods known...

example 3

Molecular Evolution Analysis

[0288]The domesticated plant or animal and wild ancestor sequences under comparison are subjected to KA / KS analysis. In this analysis, publicly or commercially available computer programs, such as Li 93 and INA, are used to determine the number of non-synonymous changes per site (KA) divided by the number of synonymous changes per site (KS) for each sequence under study as described above. Full-length coding regions or partial segments of a coding region can be used. The higher the KA / KS ratio, the more likely that a sequence has undergone adaptive evolution. Statistical significance of KA / KS values is determined using established statistic methods and available programs such as the t-test.

[0289]To further lend support to the significance of a high KA / KS ratio, the domesticated sequence under study can be compared to other evolutionarily proximate species. These comparisons allow further discrimination as to whether the adaptive evolutionary changes are u...

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Abstract

The present invention provides methods for identifying polynucleotide and polypeptide sequences which may be associated with commercially or aesthetically relevant traits in domesticated plants or animals. The methods employ comparison of homologous genes from the domesticated organism and its ancestor to identify evolutionarily significant changes and evolutionarily neutral changes. Sequences thus identified may be useful in enhancing commercially or aesthetically desirable traits in domesticated organisms or their wild ancestors.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application claims priority under 35 U.S.C. § 119 from U.S. application Ser. No. 60 / 349,088, filed Jan. 16, 2002 and U.S. application Ser. No. 60 / 315,595, filed Aug. 29, 2001. This application is also a continuation-in-part of U.S. application Ser. No. 09 / 875,666, filed Jun. 6, 2001, now U.S. Pat. No. 6,743,580, which is a continuation of U.S. application Ser. No. 09 / 368,810, filed Aug. 5, 1999, now U.S. Pat. No. 6,274,319, which is a continuation-in-part of U.S. application Ser. No. 09 / 240,915, filed Jan. 29, 1999, now U.S. Pat. No. 6,228,586, each of which is incorporated herein in its entirety by reference.TECHNICAL FIELD[0002]This invention relates to using molecular and evolutionary techniques to identify polynucleotide and polypeptide sequences corresponding to commercially or aesthetically relevant traits in domesticated plants and animals.BACKGROUND ART[0003]Humans have bred plants and animals for thousands of years, selectin...

Claims

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Application Information

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IPC IPC(8): C12Q1/68C07H21/04
CPCC12Q1/6888C12Q1/6895C12Q2600/124C12Q2600/156
Inventor MESSIER, WALTER
Owner EVOLUTIONARY GENOMICS LLC
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